Differential stabilization of adenine quartets by anions and cations

Autor: Tushar van der Wijst, F. Matthias Bickelhaupt, Célia Fonseca Guerra, Marcel Swart, Bernhard Lippert

Publikováno v: Journal of Biological Inorganic Chemistry
Journal of Biological Inorganic Chemistry-JBIC, 15(3), 387-397. Springer Verlag
van der Wijst, T, Lippert, B, Swart, M, Fonseca Guerra, C & Bickelhaupt, F M 2010, ' Differential stabilization of adenine quartets by anions and cations ', Journal of Biological Inorganic Chemistry-JBIC, vol. 15, no. 3, pp. 387-397 . https://doi.org/10.1007/s00775-009-0611-8

We have investigated the structures and stabilities of four different adenine quartets with alkali and halide ions in the gas phase and in water, using dispersion-corrected density functional theory at the BLYP-D/TZ2P level. First, we examine the emp

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::17c9f9bd8a41dacd89126845d318bde4
https://hdl.handle.net/1871/20843

Supramolecular Switches Based on the Guanine–Cytosine (GC) Watson–Crick Pair: Effect of Neutral and Ionic Substituents

Autor: Tushar van der Wijst, Célia Fonseca Guerra, F. Matthias Bickelhaupt

Publikováno v: Chemistry: A European Journal, 12(11), 3032-3042. Wiley-VCH Verlag
Guerra, C F, van der Wijst, T & Bickelhaupt, F M 2006, ' Supramolecular Switches Based on the Guanine–Cytosine (GC) Watson–Crick Pair: Effect of Neutral and Ionic Substituents ', Chemistry: A European Journal, vol. 12, no. 11, pp. 3032-3042 . https://doi.org/10.1002/chem.200501301

We have theoretically analyzed Watson-Crick guanine-cytosine (GC) base pairs in which purine-C8 and/or pyrimidine-C6 positions carry a substituent X = NH(-), NH(2), NH(3) (+) (N series), O(-), OH, or OH(2) (+) (O series), using the generalized gradie

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f4e23eadcba781280d97c19cf34462a8
https://doi.org/10.1002/chem.200501301

Adenine versus Guanine Quartets in Aqueous Solution. Dispersion-Corrected DFT Study on the Differences in π-Stacking and Hydrogen-Bonding Behavior

Autor: Marcel Swart, F. Matthias Bickelhaupt, Jordi Poater, Célia Fonseca Guerra, Tushar van der Wijst

Publikováno v: Theoretical Chemistry Accounts, 245-252. Springer New York
ISSUE=124;STARTPAGE=245;ENDPAGE=252;ISSN=1432-881X;TITLE=Theoretical Chemistry Accounts
Fonseca Guerra, C, van der Wijst, T, Poater, J, Swart, M & Bickelhaupt, F M 2010, ' Adenine versus Guanine Quartets in Aqueous Solution. Dispersion-Corrected DFT Study on the Differences in π-Stacking and Hydrogen-Bonding Behavior ', Theoretical Chemistry Accounts, no. 124, pp. 245-252 . https://doi.org/10.1007/s00214-009-0634-9

We have investigated the performance of the dispersion-corrected density functionals (BLYP-D, BP86-D and PBE-D) and the widely used B3LYP functional for describing the hydrogen bonds and the stacking interactions in DNA base dimers. For the gas-phase

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c34f7738ec981accc9243fdf8584a58b
https://research.vu.nl/en/publications/379e4144-c377-4226-889b-912c24b5804d

Rare tautomers of 1-methyluracil and 1-methylthymine: tuning relative stabilities through coordination to PtII complexes

Autor: F. Matthias Bickelhaupt, Tushar van der Wijst, Bernhard Lippert, Marcel Swart, Célia Fonseca Guerra

Publikováno v: van der Wijst, T, Guerra, C F, Swart, M, Bickelhaupt, F M & Lippert, B 2008, ' Rare Tautomers of 1-Methyluracil and 1-Methylthymine: Tuning Relative Stabilities through Coordination to Pt-II Complexes ', Chemistry: A European Journal, vol. 15, no. 1, pp. 209-218 . https://doi.org/10.1002/chem.200801476
Chemistry: A European Journal, 15(1), 209-218. Wiley-VCH Verlag

We have computationally explored how the relative stabilities of 1-methyluracil (1-MeUH) tautomers can be tuned through coordination of these tautomers to Pt(II) complexes with a particular set of ligands. This has been done using density functional

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b8969f4efe7170a7bb23cd96d06c7152
https://pubmed.ncbi.nlm.nih.gov/19058265

Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking

Autor: Tushar van der Wijst, Chris Oostenbrink, and Aldo Jongejan, Peter H. J. Keizers, Chris de Graaf, Nico P. E. Vermeulen

Publikováno v: de Graaf, C, Oostenbrink, C, Keizers, P H J, van der Wijst, T, Jongejan, A & Vermeulen, N P E 2006, ' Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking ', Journal of Medicinal Chemistry, vol. 49, no. 8, pp. 2417-30 . https://doi.org/10.1021/jm0508538
Journal of Medicinal Chemistry, 49(8), 2417-30. American Chemical Society

Automated docking strategies successfully applied to binding mode predictions of ligands in Cyt P450 crystal structures in an earlier study (de Graaf et al. J. Med. Chem. 2005, 7, 2308-2318) were used for the catalytic site prediction (CSP) of 65 sub

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5441f3bd249a880b63371a21466e1a18
https://research.vu.nl/en/publications/1b76e062-66c6-47e7-a0c2-7eb5e42c7dd0